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"Zhang, Jixian"
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DynamicBind: predicting ligand-specific protein-ligand complex structure with a deep equivariant generative model
2024
While significant advances have been made in predicting static protein structures, the inherent dynamics of proteins, modulated by ligands, are crucial for understanding protein function and facilitating drug discovery. Traditional docking methods, frequently used in studying protein-ligand interactions, typically treat proteins as rigid. While molecular dynamics simulations can propose appropriate protein conformations, they’re computationally demanding due to rare transitions between biologically relevant equilibrium states. In this study, we present DynamicBind, a deep learning method that employs equivariant geometric diffusion networks to construct a smooth energy landscape, promoting efficient transitions between different equilibrium states. DynamicBind accurately recovers ligand-specific conformations from unbound protein structures without the need for holo-structures or extensive sampling. Remarkably, it demonstrates state-of-the-art performance in docking and virtual screening benchmarks. Our experiments reveal that DynamicBind can accommodate a wide range of large protein conformational changes and identify cryptic pockets in unseen protein targets. As a result, DynamicBind shows potential in accelerating the development of small molecules for previously undruggable targets and expanding the horizons of computational drug discovery.
Proteins often function by changing conformations upon ligand binding. Efficient structural modelling of these interactions, crucial for drug discovery, is limited: here the authors address this with DynamicBind, a diffusion-based deep generative model.
Journal Article
Robust Optical and SAR Image Matching via Attention-Guided Structural Encoding and Confidence-Aware Filtering
by
Kang, Qi
,
Huang, Guoman
,
Liu, Fei
in
Accuracy
,
Artificial satellites in remote sensing
,
Attention
2025
Accurate feature matching between optical and synthetic aperture radar (SAR) images remains a significant challenge in remote sensing due to substantial modality discrepancies in texture, intensity, and geometric structure. In this study, we proposed an attention-context-aware deep learning framework (ACAMatch) for robust and efficient optical–SAR image registration. The proposed method integrates a structure-enhanced feature extractor, RS2FNet, which combines dual-stage Res2Net modules with a bi-level routing attention mechanism to capture multi-scale local textures and global structural semantics. A context-aware matching module refines correspondences through self- and cross-attention, coupled with a confidence-driven early-exit pruning strategy to reduce computational cost while maintaining accuracy. Additionally, a match-aware multi-task loss function jointly enforces spatial consistency, affine invariance, and structural coherence for end-to-end optimization. Experiments on public datasets (SEN1-2 and WHU-OPT-SAR) and a self-collected Gaofen (GF) dataset demonstrated that ACAMatch significantly outperformed existing state-of-the-art methods in terms of the number of correct matches, matching accuracy, and inference speed, especially under challenging conditions such as resolution differences and severe structural distortions. These results indicate the effectiveness and generalizability of the proposed approach for multimodal image registration, making ACAMatch a promising solution for remote sensing applications such as change detection and multi-sensor data fusion.
Journal Article
Segmentation-Based Filtering of Airborne LiDAR Point Clouds by Progressive Densification of Terrain Segments
2014
Filtering is one of the core post-processing steps for Airborne Laser Scanning (ALS) point clouds. A segmentation-based filtering (SBF) method is proposed herein. This method is composed of three key steps: point cloud segmentation, multiple echoes analysis, and iterative judgment. Moreover, the third step is our main contribution. Particularly, the iterative judgment is based on the framework of the classic progressive TIN (triangular irregular network) densification (PTD) method, but with basic processing unit being a segment rather than a single point. Seven benchmark datasets provided by ISPRS Working Group III/3 are utilized to test the SBF algorithm and the classic PTD method. Experimental results suggest that, compared with the PTD method, the SBF approach is capable of preserving discontinuities of landscapes and removing the lower parts of large objects attached on the ground surface. As a result, the SBF approach is able to reduce omission errors and total errors by 18.26% and 11.47% respectively, which would significantly decrease the cost of manual operation required in post-processing.
Journal Article
SVM-Based Classification of Segmented Airborne LiDAR Point Clouds in Urban Areas
2013
Object-based point cloud analysis (OBPA) is useful for information extraction from airborne LiDAR point clouds. An object-based classification method is proposed for classifying the airborne LiDAR point clouds in urban areas herein. In the process of classification, the surface growing algorithm is employed to make clustering of the point clouds without outliers, thirteen features of the geometry, radiometry, topology and echo characteristics are calculated, a support vector machine (SVM) is utilized to classify the segments, and connected component analysis for 3D point clouds is proposed to optimize the original classification results. Three datasets with different point densities and complexities are employed to test our method. Experiments suggest that the proposed method is capable of making a classification of the urban point clouds with the overall classification accuracy larger than 92.34% and the Kappa coefficient larger than 0.8638, and the classification accuracy is promoted with the increasing of the point density, which is meaningful for various types of applications.
Journal Article
Edge Detection and Feature Line Tracing in 3D-Point Clouds by Analyzing Geometric Properties of Neighborhoods
2016
This paper presents an automated and effective method for detecting 3D edges and tracing feature lines from 3D-point clouds. This method is named Analysis of Geometric Properties of Neighborhoods (AGPN), and it includes two main steps: edge detection and feature line tracing. In the edge detection step, AGPN analyzes geometric properties of each query point’s neighborhood, and then combines RANdom SAmple Consensus (RANSAC) and angular gap metric to detect edges. In the feature line tracing step, feature lines are traced by a hybrid method based on region growing and model fitting in the detected edges. Our approach is experimentally validated on complex man-made objects and large-scale urban scenes with millions of points. Comparative studies with state-of-the-art methods demonstrate that our method obtains a promising, reliable, and high performance in detecting edges and tracing feature lines in 3D-point clouds. Moreover, AGPN is insensitive to the point density of the input data.
Journal Article
Classification of ALS Point Cloud with Improved Point Cloud Segmentation and Random Forests
by
Ni, Huan
,
Lin, Xiangguo
,
Zhang, Jixian
in
airborne laser scanning
,
Airborne lasers
,
Classification
2017
This paper presents an automated and effective framework for classifying airborne laser scanning (ALS) point clouds. The framework is composed of four stages: (i) step-wise point cloud segmentation, (ii) feature extraction, (iii) Random Forests (RF) based feature selection and classification, and (iv) post-processing. First, a step-wise point cloud segmentation method is proposed to extract three kinds of segments, including planar, smooth and rough surfaces. Second, a segment, rather than an individual point, is taken as the basic processing unit to extract features. Third, RF is employed to select features and classify these segments. Finally, semantic rules are employed to optimize the classification result. Three datasets provided by Open Topography are utilized to test the proposed method. Experiments show that our method achieves a superior classification result with an overall classification accuracy larger than 91.17%, and kappa coefficient larger than 83.79%.
Journal Article
An Indoor Localization Method for Pedestrians Base on Combined UWB/PDR/Floor Map
2019
This paper propose a scheme for indoor pedestrian location, based on UWB (Ultra Wideband)/PDR (Pedestrian Dead Reckoning) and Floor Map data. Firstly, a robust algorithm that uses Tukey weight factor and a pathological parameter for UWB positioning is proposed. The ill-conditioned position problem is solved for a scene where UWB anchors are placed on the same elevation of a narrow corridor. Secondly, a heading angle-computed strategy of PDR is put forward. According to the UWB positioning results, the location of pedestrians is mapped to the Floor Map, and 16 possible azimuth directions with 22.5° interval in this position are designed virtually. Compared to the heading angle of PDR, the center direction of the nearest interval is adopted as the heading. However, if the difference between the head angles of PDR and the nearest map direction is less than five degrees, the heading angle of PDR is regarded as the moving heading. Thirdly, an EKF (Extended Kalman Filter) algorithm is suggested for UWB/PDR/Floor Map fusion. By utilizing the positioning results of UWB, PDR, and the possible heading angle of Floor Map, high precision positioning results are acquired. Finally, two experimental scenarios are designed in a narrow corridor and computer room at a university. The accuracy of pedestrian positioning when all the data are available is verified in the first scenario; the positioning accuracy of a situation where part of UWB is unlock is verified in the second scenario. The results show that the proposed scheme can reliably achieve decimeter-level positioning.
Journal Article
JM-Guided Sentinel 1/2 Fusion and Lightweight APM-UNet for High-Resolution Soybean Mapping
2025
What are the main findings? A lightweight and interpretable segmentation framework, APM-UNet, is proposed by integrating the Attention Sandglass Layer (ASL) for local detail enhancement and the Parallel Vision Mamba Layer (PVML) for global dependency modeling. A JM-distance-based “filter-then-learn” strategy is introduced to select multi-source and multi-temporal (Sentinel-1/2) features, effectively reducing redundancy and improving class separability in complex agricultural landscapes. What is the implication of the main finding? APM-UNet, combined with the JM-distance-based feature selection algorithm, achieved state-of-the-art accuracy (OA = 97.95%, F1 = 0.932, Kappa = 0.965, IoU = 0.799) with comparable computational cost, demonstrating excellent robustness and adaptability. This framework provides a transferable and efficient solution for fine-grained crop mapping, supporting operational applications such as agricultural monitor-ing, land-use assessment, and sustainable resource management. Accurate soybean mapping is critical for food–oil security and cropping assessment, yet spatiotemporal heterogeneity arising from fragmented parcels and phenological variability reduces class separability and robustness. This study aims to deliver a high-resolution, reusable pipeline and quantify the marginal benefits of feature selection and architecture design. We built a full-season multi-temporal Sentinel-1/2 stack and derived candidate optical/SAR features (raw bands, vegetation indices, textures, and polarimetric terms). Jeffries–Matusita (JM) distance was used for feature–phase joint selection, producing four comparable feature sets. We propose a lightweight APM-UNet: an Attention Sandglass Layer (ASL) in the shallow path to enhance texture/boundary details, and a Parallel Vision Mamba layer (PVML with Mamba-SSM) in the middle/bottleneck to model long-range/global context with near-linear complexity. Under a unified preprocessing and training/evaluation protocol, the four feature sets were paired with U-Net, SegFormer, Vision-Mamba, and APM-UNet, yielding 16 controlled configurations. Results showed consistent gains from JM-guided selection across architectures; given the same features, APM-UNet systematically outperformed all baselines. The best setup (JM-selected composite features + APM-UNet) achieved PA 92.81%, OA 97.95, Kappa 0.9649, Recall 91.42%, IoU 0.7986, and F1 0.9324, improving PA and OA by ~7.5 and 6.2 percentage points over the corresponding full-feature counterpart. These findings demonstrate that JM-guided, phenology-aware features coupled with a lightweight local–global hybrid network effectively mitigate heterogeneity-induced uncertainty, improving boundary fidelity and overall consistency while maintaining efficiency, offering a potentially transferable framework for soybean mapping in complex agricultural landscapes.
Journal Article
An Adaptive UWB/MEMS-IMU Complementary Kalman Filter for Indoor Location in NLOS Environment
2019
High precision positioning of UWB (ultra-wideband) in NLOS (non-line-of-sight) environment is one of the hot issues in the direction of indoor positioning. In this paper, a method of using a complementary Kalman filter (CKF) to fuse and filter UWB and IMU (inertial measurement unit) data and track the errors of variables such as position, speed, and direction is presented. Based on the uncertainty of magnetometer and acceleration, the noise covariance matrix of magnetometer and accelerometer is calculated dynamically, and then the weight of magnetometer data is set adaptively to correct the directional error of gyroscope. Based on the uncertainty of UWB distance observations, the covariance matrix of UWB measurement noise is calculated dynamically, and then the weight of UWB data observations is set adaptively to correct the position error. The position, velocity and direction errors are corrected by the fusion of UWB and IMU. The experimental results show that the algorithm can reduce the gyroscope deviation with magnetic noise and motion noise, so that the orientation estimates can be improved, as well as the positioning accuracy can be increased with UWB ranging noise.
Journal Article
Design and Optimization of Cluster-Based DSRC and C-V2X Hybrid Routing
2022
With the continuous development of connected and automated vehicles (CAVs) and Internet of Vehicle (IoV) technologies, various application scenarios have put forward higher requirements for vehicular communications. On the one hand, applications related to vehicle driving safety require lower latency and higher throughput. On the other hand, users who use cellular vehicle-to-everything (C-V2X) to transfer data will have to face high communication fees due to the increasing amount of data. Therefore, from the perspective of balancing quality of service (QoS) and user communication costs, this paper integrates dedicated short-range communication (DSRC) and C-V2X, two vehicular communication technologies with their own advantages, into a framework called cluster-based traffic differentiated hybrid routing (CTDHR), to provide services for in-vehicle communication. A vehicle clustering method based on hierarchical clustering is proposed to solve problems (e.g., the communication linking being difficult to maintain and the frequent cell handover due to high-speed movement of vehicles). The CTDHR framework is modeled on the resulting clusters and an objective equation was established. Finally, since the obtained objective equation is a nonlinear integer programming problem, we propose a heuristic algorithm to solve this optimization problem. In the simulation experiments, CTDHR shows better communication performance than the existing DSRC and C-V2X hybrid models. The experimental results show that CTDHR can reduce the communication costs of users while satisfying QoS.
Journal Article